Posted
by
samzenpus
on Monday December 13, 2010 @04:54AM
from the anti-coding-soap dept.

wilmavanwyk writes "In research that further bridges the biological and digital world, scientists at the University of California, San Francisco have created bacteria that can be programmed like a computer. Researchers built 'logic gates' – the building blocks of a circuit – out of genes and put them into E. coli bacteria strains. The logic gates mimic digital processing and form the basis of computational communication between cells, according to synthetic biologist Christopher A. Voigt."

But how will they be able to find "bugs" in their program when the program is all bugs?
Thank you, thank you, I'll be here all week, try the fish, the bacteria in it all programmed in Sea.... Oh I did it again!

"Today marks a milestone for the computer science and pharmaceutical industries. Partnering with one of the software industry giants, Roche Pharmaceuticals today unveiled the future of fighting rapidly mutating semi-lifeforms. Thanks to Norton Antivirus, no human body will ever be unprotected again!"

Please note that losing the ability to run or perform other activities quickly is a known and acceptable side-effect.

Wooshh... which ironically is also the sound of wanting the additional benefit from "projectile vomiting over my boss's desk"What's a few minutes mild suffering, for some payback that just keeps on giving;)

It's possible to achieve temporary projectile vomiting with lower-tech substances than programmable bacteria. Probably easier to get too, I'm pretty sure every ambulance and emergency room has them, for poisoning cases and such. I'm pretty sure you could come up with something with basic kitchen supplies, such as, I don't know, salt...

1. Programmable bacteria may not injure a human being or, through inaction, allow a human being to come to harm.2. Programmable bacteria must execute any program given to them by human beings, except where such execution would conflict with the First Law.3. Programmable bacteria must protect their own existence as long as such protection does not conflict with the First or Second Law.

1. Programmable bacteria may not injure a human being or, through inaction, allow a human being to come to harm.
2. Programmable bacteria must execute any program given to them by human beings, except where such execution would conflict with the First Law.
3. Programmable bacteria must protect their own existence as long as such protection does not conflict with the First or Second Law.

The article isn't very informative. As far as I know, you can have communication from parents to their children with genetic code. with viruses, you can also broadcast something horizontally to all individuals. From the article I get that they're trying to formalize a programming language that can control 1 individual bacteria.Honestly, it's a bit sad that I don't have time to look into the details, even if I don't know a lot about biology.

They're inserting synthetic genetic code (with known function) into E. coli that will allow individual bugs to respond in predictable ways to other bugs' chemical signals. So, for example, there is a known DNA sequence that encodes a protein that 'recognizes' signal. There is another sequence that encodes a second signal recognition protein. There is a third sequence that encodes a scaffolding that binds the two signal proteins (an AND gate), and it produces some chemical or enzymatic output. This outpu

yeah, the problem with shit like Norton is that reinstalling is the only feasible way of dealing with the threat. I do not want to reinstall my immune system, I have spent a lot of time programming it for various versions of the flue and other diseases.

tailor a bacteria to attack or compete with a bacteria which you needed to control

This already exists in the from of a virus which attacks bacteria, also known as a Bacteriophage [wikipedia.org]. It doesn't even have to be programmed from the outside to keep up with the evading, evolving bacteria; it just evolves as well. And even if you wanted to "program" this feature, you'd have to deal with the nasty problem of protein folding in silico. Better to leave this entire process highly parallel in wetware.

And even if you wanted to "program" this feature, you'd have to deal with the nasty problem of protein folding in silico. Better to leave this entire process highly parallel in wetware.

there is no need to deal with protein folding in silico - we know a LOT about proteins and how they work just from standard biochemical assays. There are literally tens of thousands of characterized molecules with known DNA sequences from which we can pick and choose useful sets - slightly modify if need be - and then recombine in novel ways inside a cell. And we can do it directly - without having to rely on some kind of directed evolution - which is quite slow. It is very hard to program a specific wel

...and how long before someone starts claiming that this has already happened and this is why we have Atlantis myths and the Black Plague? Actually, sounds like a good science fiction story for someone to write.

No matter how tight I wear my tinfoil hat, unless it is actually a full body suit and electrified on the outside, I think this will obsolete it. Imagine, cells turn cancerous if your black, gay, white, short, don't have any certain genetic or set of genetic markers. If you leave a certain atmospheric pressure, like come down off your mountain prison it reacts to a change in your body. If you pass or leave a magnetic field (or it accidentally loses power) you're a goner. I could go on and on.

While I can also think of the wonders this could allow, I think more of what could easily go wrong. When you have American scientists laughing because they gave the Russian's leukemia on accident with an early vaccine test, this doesn't make me feel any better.

It's a Dean Koontz book, to be sure. Science goes unexpectedly wrong in horrific ways. Being a Koontz book it would also need the compulsory pet dog and a strong woman the (loner/damaged) hero gets attached to.

People have been poisoning each other with both chemicals and bacteria for thousands of years; what you describe is no different.

Even the race thing. Each race is statistically more or less resistant to a given disease than others. Think smallpox in the Americas. And if you can't find a suitable genetic marker, just distribute your poison at a suitable gathering.

“At some point, Microsoft Word had to have been converted to 1s and Os. It's the same way with cells," Voigt said. "What we've done here is created a fundamental language to show that they can work in bacteria. We still have a lot fewer circuits that you could use in computers."

In the TNG episode "The Chase", it's discovered that aliens seeded the oceans of various planets with life and placed part of a computer program into the DNA distributed on each planet. When the various races (humans, vulvans, cardassians, etc) put the code together a billion years later they find an ancient race has left us a holographic message of goodwill and peace.

We Must do this! Except we change the message to play "Never gonna give you up", Rick Astley built right into the DNA of all living beings forevermore. Just waiting to be found in a billion years. Most epic troll ever.

It certainly looks like it. One interesting feature that was left out of the/. summary is that the 'wires' in the circuit are quorum sensing molecules - or signalling molecules that are sent and received by all the bacteria in a group. Except that the abstract refers to 'orthogonal' quorum sensing receivers and producers, so I guess each colony make one compound and senses another? Interesting stuff.

The orthogonal refers to the fact that the molecule is not naturally part of the E. coli sensing system - and so the synthetic 'message' is not convoluted or otherwise disturbed by the natural processes already taking place in the E. coli. So yes, this would allow individual cells or populations to pass different bits. You cold have as many bits of information as you found 'orthogonal' signaling molecules.

concerned about this? Oh sure, it won't get out of hand...just like the creation of the A-bomb
didn't get out of hand. This one is more scary because it is bacteria.
I thought we outlawed germ warfare (even though we know both sides kept up the research).

Instead of having bugs in our programs, we are going to have programs in bugs. What would happen if it supports recursion? Is it possible we humans have been looking down the call stack instead of up? OMG indeed. OMG is just one step up the call stack! OMG'sG!!!!

The ability to encode arbitrary information in DNA has applications in security and encryption.

Let's say Alice wants to send a plaintext message to Bob. Except with DNA it's always Bob sending plaintext DNA to Alice. OK I have to correct a little bit and replace "Alice" with "Bob" and "Bob" with "Alice"... eh, that didn't work because it replaced all the strings with "Alice".... ctrl-Z ctrl-Z ok let's do this right... first replace "Bob" with a swap like "Sue"... replace "Alice" with "Bob"... wait a seco

One of the lines had the "mad scientist's" mum asking why on earth he'd want to make bacteria smart? The hero asked his mother, "Why are you so worried?" She answered, "Ask anyone that's ever cleaned a toilet bowl."